src.imagedata.transports package

Submodules

src.imagedata.transports.abstracttransport module

Abstract class for image transports.

Defines generic functions.

class src.imagedata.transports.abstracttransport.AbstractTransport(name: str, description: str, authors: str, version: str, url: str, schemes: List[str] | None = None)[source]

Bases: object

Abstract base class definition for imagedata transport plugins. Plugins must be a subclass of AbstractPlugin and must define the attributes set in __init__() and the following methods:

open() method isfile() method walk() method

property authors: str

Plugin authors

Multi-line string naming the author(s) of the plugin.

abstract close()[source]

Close the transport

property description: str

Plugin description

Single line string describing the transport method.

abstract exists(path: str) → bool[source]

Determine whether the named path exists.

abstract info(path) → str[source]

Return info describing the object

Parameters:

path (str) – object path

Returns:

Preferably a one-line string describing the object

Return type:

description (str)

abstract isfile(path: str) → bool[source]

Return True if path is an existing regular file.

mimetype = '*'
property name: str

Plugin name

Single word string describing the image format. Typical names: file, dicom, xnat

abstract open(path: str, mode: str = 'r') → IOBase[source]

Extract a member from the archive as a file-like object.

plugin_type = 'transport'
property schemes: List[str]

List of transport schemes supported by this plugin.

List of strings.

property url: str

Plugin URL

URL string to the site of the plugin or the author(s).

property version: str

Plugin version

String giving the plugin version. Version scheme: 1.0.0

abstract walk(top: str)[source]

Generate the file names in a directory tree by walking the tree. Input: - top: starting point for walk (str) Return: - tuples of (root, dirs, files)

exception src.imagedata.transports.abstracttransport.NoOtherInstance[source]

Bases: Exception

src.imagedata.transports.dicomtransport module

Transfer DICOM images to and from DICOM Storage SCP

exception src.imagedata.transports.dicomtransport.AssociationFailed[source]

Bases: Exception

exception src.imagedata.transports.dicomtransport.AssociationNotEstablished[source]

Bases: Exception

class src.imagedata.transports.dicomtransport.DicomTransport(netloc: str | None = None, root: str | None = None, mode: str | None = 'r', read_directory_only: bool | None = False, opts: dict | None = None)[source]

Bases: AbstractTransport

Send DICOM images to DICOM Storage SCP

authors = 'Erling Andersen'
close()[source]

Close the DICOM association transport

description = 'Receive/Send DICOM images to DICOM Storage SCP.'
exists(path)[source]

Determine whether the named path exists.

info(path) → str[source]

Return info describing the object

Parameters:

path (str) – object path

Returns:

Preferably a one-line string describing the object

Return type:

description (str)

isfile(path)[source]

Return True if path is an existing regular file.

name = 'dicom'
open(path, mode='r')[source]

Extract a member from the archive as a file-like object.

schemes = ['dicom']
store(ds)[source]

Store DICOM dataset using DICOM Storage SCU protocol.

url = 'www.helse-bergen.no'
version = '2.0.0'
walk(top)[source]

Generate the file names in a directory tree by walking the tree. Input: - top: starting point for walk (str) Return: - tuples of (root, dirs, files)

src.imagedata.transports.filetransport module

Read/Write local files

class src.imagedata.transports.filetransport.FileTransport(netloc: str | None = None, root: str | None = None, mode: str | None = 'r', read_directory_only: bool | None = False, opts: dict | None = None)[source]

Bases: AbstractTransport

Read/write local files.

Parameters:

  • netloc (str) – Not used.

  • root (str) – Root path.

  • mode (str) – Filesystem access mode.

  • read_directory_only (bool) – Whether root should refer to a directory.

  • opts (dict) – Options

Returns:

FileTransport instance

Raises:

  • RootIsNotDirectory – when the root is not a directory when read_directory_only is True.

  • FileNotFoundError – Specified root does not exist.

  • AssertionError – When root is None.

authors: str = 'Erling Andersen'
close()[source]

Close the transport

description: str = 'Read and write local files.'
exists(path)[source]

Determine whether the named path exists.

info(path) → str[source]

Return info describing the object

Parameters:

path (str) – object path

Returns:

Preferably a one-line string describing the object

Return type:

description (str)

isfile(path)[source]

Check whether path refers to an existing regular file.

Parameters:

path – Path to file.

Returns:

Existense of regular file (bool)

name: str = 'file'
netloc: str = None
open(path: str, mode: str = 'r') → IOBase[source]

Extract a member from the archive as a file-like object.

Parameters:

  • path (str) – Path to file.

  • mode (str) – Open mode, can be ‘r’, ‘w’, ‘x’ or ‘a’

opts: dict = None
path: str = None
schemes: List[str] = ['file']
url: str = 'www.helse-bergen.no'
version: str = '1.1.0'
walk(top)[source]

Generate the file names in a directory tree by walking the tree.

Parameters:

top – starting point for walk (str)

Returns:

tuples of (root, dirs, files)

src.imagedata.transports.xnattransport module

Read/write files in xnat database

class src.imagedata.transports.xnattransport.XnatTransport(netloc: str | None = None, root: str | None = None, mode: str | None = 'r', read_directory_only: bool | None = False, opts: dict | None = None)[source]

Bases: AbstractTransport

Read/write files in xnat database.

authors: str = 'Erling Andersen'
close()[source]

Close the transport

description: str = 'Read and write files in xnat database.'
exists(path)[source]

Return True if the named path exists.

info(path) → str[source]

Return info describing the object

Parameters:

path (str) – object path

Returns:

Preferably a one-line string describing the object

Return type:

description (str)

isfile(path)[source]

Return True if path is an existing regular file.

mimetype: str = 'application/zip'
name: str = 'xnat'
netloc: str = None
open(path, mode='r')[source]

Extract a member from the archive as a file-like object.

opts: [<class 'dict'>] = None
read_directory_only: bool = None
schemes: List[str] = ['xnat']
url: str = 'www.helse-bergen.no'
version: str = '2.0.0'
walk(top)[source]

Generate the file names in a directory tree by walking the tree. Input: - top: starting point for walk (str) Return: - tuples of (root, dirs, files)

Module contents

This module provides plugins for various image transports.

Standard plugins provides support for file, http/https and xnat transports.

exception src.imagedata.transports.FunctionNotSupported[source]

Bases: Exception

exception src.imagedata.transports.RootIsNotDirectory[source]

Bases: Exception

src.imagedata.transports.Transport(scheme, netloc=None, root=None, mode='r', read_directory_only=False, opts=None)[source]

Return plugin for given transport scheme.

exception src.imagedata.transports.TransportPluginNotFound[source]

Bases: Exception

src.imagedata.transports.get_transporter_list()[source]